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Development

This page covers integrating CORE as a library, building from source, running tests, creating executables, and packaging.

PyPI Integration

CORE is available as a Python package for direct integration into data pipelines.

pip install cdisc-rules-engine

This allows you to:

  • Import the rules engine library into your Python projects
  • Validate data without requiring XPT format files
  • Integrate rules validation into existing pipelines

For implementation details, see PYPI.md.

Environment Setup

Python 3.12 is required. Other versions are not supported and may produce unexpected errors or incorrect validation results.

# Check your Python version
python --version

# Clone the repository
git clone https://github.com/cdisc-org/cdisc-rules-engine.git
cd cdisc-rules-engine

# Create a virtual environment
python -m venv venv

# If you have multiple Python versions, be explicit:
# python3.12 -m venv venv

# Activate (Linux/Mac)
source venv/bin/activate

# Activate (Windows)
.\venv\Scripts\Activate

# Install dependencies
python -m pip install -r requirements-dev.txt

Running Tests

From the project root, run both unit and regression tests:

python -m pytest tests

Creating an Executable

Pre-built executables are available on the Releases page. If you need to build your own, see README_Build_Executable.md in the repository root.

For reference, the PyInstaller commands are:

Linux:

pyinstaller core.py \
  --add-data=venv/lib/python3.12/site-packages/xmlschema/schemas:xmlschema/schemas \
  --add-data=resources/cache:resources/cache \
  --add-data=resources/templates:resources/templates \
  --add-data=resources/jsonata:resources/jsonata

Windows:

pyinstaller core.py ^
  --add-data=".venv/Lib/site-packages/xmlschema/schemas;xmlschema/schemas" ^
  --add-data="resources/cache;resources/cache" ^
  --add-data="resources/templates;resources/templates" ^
  --add-data="resources/jsonata;resources/jsonata"

The executable is created in the dist/ folder and does not require Python to be installed on the target machine.

Creating a Python Package (.whl)

All non-Python files must be listed in MANIFEST.in to be included in the distribution.

Unix / Mac:

python3 -m pip install --upgrade build
python3 -m build

Install locally from the dist/ folder:

pip3 install dist/cdisc_rules_engine-{version}-py3-none-any.whl

Upload to PyPI:

python3 -m pip install --upgrade twine
python3 -m twine upload --repository {repository_name} dist/*

Windows:

py -m pip install --upgrade build
py -m build

Install locally:

pip install dist\cdisc_rules_engine-{version}-py3-none-any.whl

Upload to PyPI:

py -m pip install --upgrade twine
py -m twine upload --repository {repository_name} dist/*

Updating the USDM JSON Schema

CORE validates against USDM JSON Schema versions 3.0 and 4.0. Schema definitions are stored as .pkl files in resources/cache/:

  • resources/cache/usdm-3-0-schema.pkl
  • resources/cache/usdm-4-0-schema.pkl

These are derived from the OpenAPI specs in cdisc-org/DDF-RA. To update or add a schema version:

  1. Extract the OpenAPI spec for the target tag:

    git --no-pager --git-dir DDF-RA.git show --format=format:"%B" {tag}:Deliverables/API/USDM_API.json > USDM_API_{version}.json

    Example tag: v3.0.0

  2. Convert the OpenAPI spec to JSON Schema:

    python scripts/openapi-to-json.py

  3. Convert the JSON Schema to .pkl:

    python scripts/json_pkl_converter.py

  4. Place the resulting .pkl file in resources/cache/.

Dataset Format Reference (JSON)

When validating a single rule with --local-rules, JSON datasets must match the Dataset-JSON format used by the rule editor:

{
  "datasets": [
    {
      "filename": "cm.xpt",
      "label": "Concomitant/Concurrent medications",
      "domain": "CM",
      "variables": [
        {
          "name": "STUDYID",
          "label": "Study Identifier",
          "type": "Char",
          "length": 10
        }
      ],
      "records": {
        "STUDYID": ["CDISC-TEST", "CDISC-TEST", "CDISC-TEST", "CDISC-TEST"]
      }
    }
  ]
}